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Table 5 Valid and correct alignments using needle.

From: libgapmis: extending short-read alignments

Programme Species Length of queries [bp] Gap occurrence frequency Gap opening penalty Gap extension penalty Valid alignments Correct alignments
needle AT 100 2.4 × 10-5 10.0 0.5 99,988 99,917
needle AT 100 2.4 × 10-5 15.0 0.5 99,992 99,911
needle AT 100 2.4 × 10-5 20.0 0.5 99,996 99,850
needle AT 150 2.4 × 10-5 10.0 0.5 99,991 99,919
needle AT 150 2.4 × 10-5 15.0 0.5 99,992 99,901
needle AT 150 2.4 × 10-5 20.0 0.5 99,996 99,834
  1. The valid and correct alignments of 100, 000 pairs of simulated sequences with the gap occurrence frequency observed in Arabidopsis thaliana using needle. Each of the datasets consists of 100,000 pairs of sequences; the highest numbers of correct and valid alignments for each dataset are shown in bold.